RPS-BLAST 2.2.26 [Sep-21-2011]
Database: CDD.v3.10
44,354 sequences; 10,937,602 total letters
Searching..................................................done
Query= psy8855
(200 letters)
>gnl|CDD|183087 PRK11325, PRK11325, scaffold protein; Provisional.
Length = 127
Score = 220 bits (562), Expect = 1e-74
Identities = 85/97 (87%), Positives = 91/97 (93%)
Query: 1 MSYSEKVLDHYENPRNVGVFEKNDNTVGTGMVGAPACGDVMKLQIKVNKNGVITDAKFKT 60
M+YSEKV+DHYENPRNVG F+KND VGTGMVGAPACGDVMKLQIKVN G+I DAKFKT
Sbjct: 1 MAYSEKVIDHYENPRNVGSFDKNDPNVGTGMVGAPACGDVMKLQIKVNDEGIIEDAKFKT 60
Query: 61 YGCGSAIASSSLVTEWVKGKTLDEAMSIKNTDIAEEL 97
YGCGSAIASSSLVTEWVKGKTLDEA++IKNTDIAEEL
Sbjct: 61 YGCGSAIASSSLVTEWVKGKTLDEALAIKNTDIAEEL 97
>gnl|CDD|188192 TIGR01999, iscU, FeS cluster assembly scaffold IscU. This model
represents IscU, a homolog of the N-terminal region of
NifU, an Fe-S cluster assembly protein found mostly in
nitrogen-fixing bacteria. IscU is considered part of
the IscSUA-hscAB-fdx system of Fe-S assembly, whereas
NifU is found in nitrogenase-containing
(nitrogen-fixing) species. A NifU-type protein is also
found in Helicobacter and Campylobacter. IscU and NifU
are considered scaffold proteins on which Fe-S clusters
are assembled before transfer to apoproteins. This
model excludes true NifU proteins as in Klebsiella
pneumoniae and Anabaena sp. as well as archaeal
homologs. It includes largely proteobacterial and
eukaryotic forms [Biosynthesis of cofactors, prosthetic
groups, and carriers, Other].
Length = 124
Score = 185 bits (471), Expect = 7e-61
Identities = 73/95 (76%), Positives = 86/95 (90%)
Query: 3 YSEKVLDHYENPRNVGVFEKNDNTVGTGMVGAPACGDVMKLQIKVNKNGVITDAKFKTYG 62
YSEKV+DHYENPRNVG +K+D VGTG+VGAPACGDVMKLQIKVN +G+I DAKFKT+G
Sbjct: 1 YSEKVIDHYENPRNVGSLDKDDKNVGTGLVGAPACGDVMKLQIKVNDDGIIEDAKFKTFG 60
Query: 63 CGSAIASSSLVTEWVKGKTLDEAMSIKNTDIAEEL 97
CGSAIASSSL TE +KGK+L+EA+ IKNT+IA+EL
Sbjct: 61 CGSAIASSSLATELIKGKSLEEALKIKNTEIAKEL 95
>gnl|CDD|216592 pfam01592, NifU_N, NifU-like N terminal domain. This domain is
found in NifU in combination with pfam01106. This
domain is found on isolated in several bacterial
species. The nif genes are responsible for nitrogen
fixation. However this domain is found in bacteria that
do not fix nitrogen, so it may have a broader
significance in the cell than nitrogen fixation. These
proteins appear to be scaffold proteins for iron-sulfur
clusters.
Length = 126
Score = 162 bits (413), Expect = 6e-52
Identities = 67/97 (69%), Positives = 77/97 (79%), Gaps = 4/97 (4%)
Query: 3 YSEKVLDHYENPRNVGVFEKNDNTVGTGMVGAPACGDVMKLQIKVN-KNGVITDAKFKTY 61
YS+KVLDH++NPRNVGV E+ D G VG+PACGD M+LQIKV+ I DAKFKT+
Sbjct: 2 YSDKVLDHFKNPRNVGVLEEAD---AVGDVGSPACGDAMRLQIKVDEDTDRIEDAKFKTF 58
Query: 62 GCGSAIASSSLVTEWVKGKTLDEAMSIKNTDIAEELV 98
GCGSAIASSS +TE VKGKTLDEA+ I NTDIAEEL
Sbjct: 59 GCGSAIASSSALTELVKGKTLDEALKITNTDIAEELG 95
>gnl|CDD|223892 COG0822, IscU, NifU homolog involved in Fe-S cluster formation
[Energy production and conversion].
Length = 150
Score = 143 bits (362), Expect = 6e-44
Identities = 64/99 (64%), Positives = 77/99 (77%), Gaps = 5/99 (5%)
Query: 1 MSYSEKVLDHYENPRNVGVFEKNDNTVGTGMVGAPACGDVMKLQIKVNKNGVITDAKFKT 60
YSEK+LDHY+NPRNVGV + D VG G VGAPACGDV+ L +KV+ NGVI DAKFK
Sbjct: 5 DLYSEKILDHYKNPRNVGVLDDAD--VGVGHVGAPACGDVITLYLKVD-NGVIEDAKFKG 61
Query: 61 YGCGSAIASSSLVTEWVKGKTLDEAMSIK--NTDIAEEL 97
+GC +IASSS++TE VKGKTLDEA+ I TD+A+EL
Sbjct: 62 FGCAISIASSSMMTELVKGKTLDEALKITEAFTDMAKEL 100
>gnl|CDD|143480 cd06664, IscU_like, Iron-sulfur cluster scaffold-like proteins.
IscU_like and NifU_like proteins. IscU and NifU
function as a scaffold for the assembly of [2Fe-2S]
clusters before they are transferred to apo target
proteins. They are highly conserved and play vital
roles in the ISC and NIF systems of Fe-S protein
maturation. NIF genes participate in nitrogen fixation
in several isolated bacterial species. The NifU domain,
however, is also found in bacteria that do not fix
nitrogen, so it may have wider significance in the
cell. Human IscU interacts with frataxin, the
Friedreich ataxia gene product, and incorrectly spliced
IscU has been shown to disrupt iron homeostasis in
skeletal muscle and cause myopathy.
Length = 123
Score = 138 bits (351), Expect = 1e-42
Identities = 55/94 (58%), Positives = 67/94 (71%), Gaps = 4/94 (4%)
Query: 3 YSEKVLDHYENPRNVGVFEKNDNTVGTGMVGAPACGDVMKLQIKVNKNGVITDAKFKTYG 62
YSE +LDHY NPRNVG E D GTG VG P CGD + L +KV +G ITDAKF+ +G
Sbjct: 2 YSEIILDHYRNPRNVGRLEDAD---GTGEVGNPLCGDEITLYLKVE-DGRITDAKFQGFG 57
Query: 63 CGSAIASSSLVTEWVKGKTLDEAMSIKNTDIAEE 96
C +IAS+SL+TE +KGKTLDEA+ + N DIA
Sbjct: 58 CAISIASASLLTELIKGKTLDEALKLLNKDIAML 91
>gnl|CDD|132460 TIGR03419, NifU_clost, FeS cluster assembly scaffold protein NifU,
Clostridium type. NifU and NifS form a pair of
iron-sulfur (FeS) cluster biosynthesis proteins much
simpler than the ISC and SUF systems. Members of this
protein family are a distinct group of NifU-like
proteins, found always to a NifS-like protein and
restricted to species that lack a SUF system. Typically,
NIF systems service a smaller number of FeS-containing
proteins than do ISC or SUF. Members of this particular
branch typically are found, almost half the time, near
the mnmA gene, involved in the carboxymethylaminomethyl
modification of U34 in some tRNAs (see GenProp0704).
While other NifU proteins are associated with nitrogen
fixation, this family is not [Biosynthesis of cofactors,
prosthetic groups, and carriers, Other].
Length = 121
Score = 130 bits (329), Expect = 3e-39
Identities = 61/125 (48%), Positives = 77/125 (61%), Gaps = 17/125 (13%)
Query: 3 YSEKVLDHYENPRNVGVFEKNDNTVGTGMVGAPACGDVMKLQIKVNKNGVITDAKFKTYG 62
YSEKV+DH+ NPRNVG E D G G VG P CGD+MK+ +KV ++ +I D KFKT+G
Sbjct: 1 YSEKVMDHFMNPRNVGEIENAD---GVGEVGNPKCGDIMKIFLKV-EDDIIKDVKFKTFG 56
Query: 63 CGSAIASSSLVTEWVKGKTLDEAMSIKNTDIAEELVTKKAAKY-------------INKY 109
CG+AIASSS+ TE +KGKTL+EA + N +AE L K IN Y
Sbjct: 57 CGAAIASSSMATEMIKGKTLEEAWELTNKAVAEALDGLPPVKMHCSVLAEEAIHKAINDY 116
Query: 110 IQKRG 114
+K G
Sbjct: 117 REKNG 121
>gnl|CDD|213674 TIGR02011, IscA, iron-sulfur cluster assembly protein IscA. This
model represents the IscA component of the ISC system
for iron-sulfur cluster assembly. The ISC system
consists of IscRASU, HscAB and an Isc-specific
ferredoxin. IscA previously was believed to act as a
scaffold and now is seen as an iron donor protein. This
clade is limited to the proteobacteria [Biosynthesis of
cofactors, prosthetic groups, and carriers, Other].
Length = 105
Score = 129 bits (327), Expect = 3e-39
Identities = 55/103 (53%), Positives = 75/103 (72%)
Query: 98 VTKKAAKYINKYIQKRGKGIGLRLGVYNRGCSGLSYKLEYVDEKRKEDQVFKLNGVQIFI 157
+T AA +N ++ RGKG GLRLGV GCSG++Y LE+VDE +D VF+ GV+I I
Sbjct: 3 LTDSAAARVNTFLANRGKGFGLRLGVKTSGCSGMAYVLEFVDEPTPDDIVFEDKGVKIVI 62
Query: 158 NEKDLLYFNGIELDFEFDGLNKGFKFKNPNIKNKCGCGKSFQI 200
+ K L Y +G +LDF +GLN+GFKF NPN+K++CGCG+SF +
Sbjct: 63 DGKSLQYLDGTQLDFVKEGLNEGFKFTNPNVKDECGCGESFHV 105
>gnl|CDD|223393 COG0316, sufA, Fe-S cluster assembly scaffold protein
[Posttranslational modification, protein turnover,
chaperones].
Length = 110
Score = 129 bits (327), Expect = 4e-39
Identities = 46/104 (44%), Positives = 66/104 (63%), Gaps = 1/104 (0%)
Query: 98 VTKKAAKYINKYIQKRG-KGIGLRLGVYNRGCSGLSYKLEYVDEKRKEDQVFKLNGVQIF 156
+T AA + + K G + +GLR+GV GCSG Y LE+ DE ++D VF+ +GV++
Sbjct: 7 LTDAAAARVKALLAKEGEENLGLRVGVKGGGCSGFQYGLEFDDEINEDDTVFEQDGVKVV 66
Query: 157 INEKDLLYFNGIELDFEFDGLNKGFKFKNPNIKNKCGCGKSFQI 200
++ K L Y G E+D+ D L GF FKNPN K+ CGCG+SF +
Sbjct: 67 VDPKSLPYLEGTEIDYVEDLLGSGFTFKNPNAKSSCGCGESFSV 110
>gnl|CDD|181914 PRK09502, iscA, iron-sulfur cluster assembly protein; Provisional.
Length = 107
Score = 122 bits (307), Expect = 3e-36
Identities = 52/103 (50%), Positives = 75/103 (72%)
Query: 98 VTKKAAKYINKYIQKRGKGIGLRLGVYNRGCSGLSYKLEYVDEKRKEDQVFKLNGVQIFI 157
++ AA +N ++ RGKG GLRLGV GCSG++Y LE+VDE ED VF+ GV++ +
Sbjct: 5 LSDSAAARVNTFLANRGKGFGLRLGVRTSGCSGMAYVLEFVDEPTPEDIVFEDKGVKVVV 64
Query: 158 NEKDLLYFNGIELDFEFDGLNKGFKFKNPNIKNKCGCGKSFQI 200
+ K L + +G +LDF +GLN+GFKF NPN+K++CGCG+SF +
Sbjct: 65 DGKSLQFLDGTQLDFVKEGLNEGFKFTNPNVKDECGCGESFHV 107
>gnl|CDD|232799 TIGR00049, TIGR00049, Iron-sulfur cluster assembly accessory
protein. Proteins in this subfamily appear to be
associated with the process of FeS-cluster assembly. The
HesB proteins are associated with the nif gene cluster
and the Rhizobium gene IscN has been shown to be
required for nitrogen fixation. Nitrogenase includes
multiple FeS clusters and many genes for their assembly.
The E. coli SufA protein is associated with SufS, a NifS
homolog and SufD which are involved in the FeS cluster
assembly of the FhnF protein. The Azotobacter protein
IscA (homologs of which are also found in E.coli) is
associated which IscS, another NifS homolog and IscU, a
nifU homolog as well as other factors consistent with a
role in FeS cluster chemistry. A homolog from Geobacter
contains a selenocysteine in place of an otherwise
invariant cysteine, further suggesting a role in redox
chemistry [Biosynthesis of cofactors, prosthetic groups,
and carriers, Other].
Length = 105
Score = 120 bits (303), Expect = 1e-35
Identities = 47/104 (45%), Positives = 67/104 (64%), Gaps = 1/104 (0%)
Query: 98 VTKKAAKYINKYIQKRGK-GIGLRLGVYNRGCSGLSYKLEYVDEKRKEDQVFKLNGVQIF 156
+T AAK I + G+ +GLR+GV GCSGL Y LE+ DE ++D+VF+ +GV++
Sbjct: 2 LTDSAAKRIKALLAGEGEPNLGLRVGVKGGGCSGLQYGLEFDDEPNEDDEVFEQDGVKVV 61
Query: 157 INEKDLLYFNGIELDFEFDGLNKGFKFKNPNIKNKCGCGKSFQI 200
++ K L Y +G E+D+ + L GF F NPN K CGCGKSF +
Sbjct: 62 VDPKSLPYLDGSEIDYVEELLGSGFTFTNPNAKGTCGCGKSFSV 105
>gnl|CDD|233679 TIGR02000, NifU_proper, Fe-S cluster assembly protein NifU.
Three different but partially homologous Fe-S cluster
assembly systems have been described: Isc, Suf, and
Nif. The latter is associated with donation of an Fe-S
cluster to nitrogenase in a number of nitrogen-fixing
species. NifU, described here, consists of an
N-terminal domain (pfam01592) and a C-terminal domain
(pfam01106). Homologs with an equivalent domain
archictecture from Helicobacter and Campylobacter,
however, are excluded from this model by a high trusted
cutoff. The model, therefore, is specific for NifU
involved in nitrogenase maturation. The related model
TIGR01999 homologous to the N-terminus of this model
describes IscU from the Isc system as in E. coli,
Saccharomyces cerevisiae, and Homo sapiens
[Biosynthesis of cofactors, prosthetic groups, and
carriers, Other, Central intermediary metabolism,
Nitrogen fixation].
Length = 290
Score = 117 bits (294), Expect = 3e-32
Identities = 48/96 (50%), Positives = 69/96 (71%), Gaps = 4/96 (4%)
Query: 3 YSEKVLDHYENPRNVGVFEKNDNTVGTGMVGAPACGDVMKLQIKVN-KNGVITDAKFKTY 61
Y++KV +H+ NP+N GV E + G VG+ +CGD ++L +KV+ ++ I DA F+T+
Sbjct: 4 YTDKVKEHFYNPKNAGVVEDANAV---GEVGSISCGDALRLMLKVDPESDKIVDAGFQTF 60
Query: 62 GCGSAIASSSLVTEWVKGKTLDEAMSIKNTDIAEEL 97
GCGSAIASSS +TE +KG TLDEA+ + N DIA+ L
Sbjct: 61 GCGSAIASSSALTEMIKGLTLDEALKVSNQDIADYL 96
>gnl|CDD|110518 pfam01521, Fe-S_biosyn, Iron-sulphur cluster biosynthesis. This
family is involved in iron-sulphur cluster biosynthesis.
Its members include proteins that are involved in
nitrogen fixation such as the HesB and HesB-like
proteins.
Length = 91
Score = 104 bits (262), Expect = 1e-29
Identities = 40/89 (44%), Positives = 54/89 (60%)
Query: 98 VTKKAAKYINKYIQKRGKGIGLRLGVYNRGCSGLSYKLEYVDEKRKEDQVFKLNGVQIFI 157
+T AAK+I K + G GLR+GV GCSG SY L + DE + D+VF+ +GV + +
Sbjct: 3 LTDAAAKHIKKLLDLEGGENGLRIGVRYGGCSGFSYGLTFEDEPDEGDEVFEQDGVTVVV 62
Query: 158 NEKDLLYFNGIELDFEFDGLNKGFKFKNP 186
+EK L Y G E+DF + L GF F NP
Sbjct: 63 DEKSLPYLEGTEIDFVEELLGSGFTFSNP 91
>gnl|CDD|131052 TIGR01997, sufA_proteo, FeS assembly scaffold SufA. This model
represents the SufA protein of the SUF system of
iron-sulfur cluster biosynthesis. This system performs
FeS biosynthesis even during oxidative stress and tends
to be absent in obligate anaerobic and microaerophilic
bacteria [Biosynthesis of cofactors, prosthetic groups,
and carriers, Other].
Length = 107
Score = 99.5 bits (248), Expect = 3e-27
Identities = 40/102 (39%), Positives = 67/102 (65%)
Query: 99 TKKAAKYINKYIQKRGKGIGLRLGVYNRGCSGLSYKLEYVDEKRKEDQVFKLNGVQIFIN 158
T AA +I + + KR + +G+RLGV GC+G+ Y L+ V E +K+D + + +G ++F+
Sbjct: 6 TDAAAIHIRELVAKRPEAVGIRLGVKKTGCAGMEYVLDLVSEPKKDDDLIEHDGAKVFVA 65
Query: 159 EKDLLYFNGIELDFEFDGLNKGFKFKNPNIKNKCGCGKSFQI 200
+ +L+ G ++DF L +GFKF NPN + CGCG+SF++
Sbjct: 66 PEAVLFILGTQVDFVRTTLRQGFKFNNPNATSACGCGESFEL 107
>gnl|CDD|181915 PRK09504, sufA, iron-sulfur cluster assembly scaffold protein;
Provisional.
Length = 122
Score = 95.2 bits (237), Expect = 2e-25
Identities = 41/103 (39%), Positives = 67/103 (65%)
Query: 98 VTKKAAKYINKYIQKRGKGIGLRLGVYNRGCSGLSYKLEYVDEKRKEDQVFKLNGVQIFI 157
+T AA +I + + K+ G+RLGV GC+G Y L+ V E K+D VF+ +G ++F+
Sbjct: 20 LTPAAAAHIRELMAKQPGMKGVRLGVKQTGCAGFGYVLDSVSEPDKDDLVFEHDGAKLFV 79
Query: 158 NEKDLLYFNGIELDFEFDGLNKGFKFKNPNIKNKCGCGKSFQI 200
+ + + +G E+D+ +GLN+ FKF NP +N+CGCG+SF +
Sbjct: 80 PLQAMPFIDGTEVDYVREGLNQIFKFHNPKAQNECGCGESFGV 122
>gnl|CDD|233676 TIGR01994, SUF_scaf_2, SUF system FeS assembly protein, NifU
family. Three iron-sulfur cluster assembly systems are
known so far. ISC is broadly distributed while NIF
tends to be associated with nitrogenase in
nitrogen-fixing bacteria. The most recently described
is SUF, believed to be important to maintain the
function during aerobic stress of enzymes with labile
Fe-S clusters. It is fairly widely distributed. This
family represents one of two different proteins
proposed to act as a scaffold on which the Fe-S cluster
is built and from which it is transferred [Biosynthesis
of cofactors, prosthetic groups, and carriers, Other].
Length = 137
Score = 77.0 bits (190), Expect = 3e-18
Identities = 36/86 (41%), Positives = 53/86 (61%), Gaps = 4/86 (4%)
Query: 3 YSEKVLDHYENPRNVGVFEKNDNTVGTGMVGAPACGDVMKLQIKVNKNGVITDAKFKTYG 62
Y + +LDHY+NPR+ G E D TV P CGD + L +K+ I D F+ G
Sbjct: 5 YRQVILDHYKNPRHRGKLE--DATVQERGHN-PTCGDEITLTVKLE-GDRIEDIAFEGEG 60
Query: 63 CGSAIASSSLVTEWVKGKTLDEAMSI 88
C + AS+S++TE +KGKT++EA+S+
Sbjct: 61 CSISQASASMMTELIKGKTVEEALSL 86
>gnl|CDD|184186 PRK13623, PRK13623, iron-sulfur cluster insertion protein ErpA;
Provisional.
Length = 115
Score = 63.4 bits (155), Expect = 2e-13
Identities = 39/106 (36%), Positives = 56/106 (52%), Gaps = 7/106 (6%)
Query: 99 TKKAAKYINKYIQKRGKG-IGLRLGVYNRGCSGLSYKLEYVDEKRKEDQ-VFKLNGVQIF 156
T AA + + I++ G + LR+ + GCSG Y + DE+ ED + GV +
Sbjct: 13 TDAAAAKVKELIEEEGNPDLKLRVYITGGGCSGFQYGFTF-DEQVNEDDTTIEKQGVTLV 71
Query: 157 INEKDLLYFNGIELDFEFDGLNKGFKF--KNPNIKNKCGCGKSFQI 200
++ L Y G E+D+ +GL G +F KNPN K CGCG SF I
Sbjct: 72 VDPMSLQYLVGAEVDYT-EGLE-GSRFVIKNPNAKTTCGCGSSFSI 115
>gnl|CDD|215564 PLN03082, PLN03082, Iron-sulfur cluster assembly; Provisional.
Length = 163
Score = 52.2 bits (125), Expect = 9e-09
Identities = 25/87 (28%), Positives = 42/87 (48%), Gaps = 1/87 (1%)
Query: 115 KGIGLRLGVYNRGCSGLSYKLEYVDEKRKEDQVFKLNGVQIFINEKDLLYFNGIELDFEF 174
+ LRL V GCSG Y E D+ +D+VF+ +GV++ ++ + G +D+
Sbjct: 76 EDKMLRLSVETGGCSGFQYVFELDDKTNSDDRVFEKDGVKLVVDNISYDFVKGATVDYVE 135
Query: 175 DGLNKGFKFK-NPNIKNKCGCGKSFQI 200
+ + F NP+ C C SF +
Sbjct: 136 ELIRSAFVVSTNPSAVGGCSCKSSFMV 162
>gnl|CDD|132384 TIGR03341, YhgI_GntY, IscR-regulated protein YhgI. IscR
(TIGR02010) is an iron-sulfur cluster-binding
transcriptional regulator (see Genome Property
GenProp0138). Members of this protein family include
YhgI, whose expression is under control of IscR, and
show sequence similarity to IscA, a known protein of
iron-sulfur cluster biosynthesis. These two lines of
evidence strongly suggest a role as an iron-sulfur
cluster biosynthesis protein. An older study designated
this protein GntY and suggested a role for it and for
the product of an adjacent gene, based on
complementation studies, in gluconate utilization
[Biosynthesis of cofactors, prosthetic groups, and
carriers, Other].
Length = 190
Score = 40.8 bits (96), Expect = 1e-04
Identities = 25/96 (26%), Positives = 41/96 (42%), Gaps = 6/96 (6%)
Query: 98 VTKKAAKYINKYIQKRGKGIGLRLGVYNRGCS----GLSYKLEYVDEKRKEDQVFKLNGV 153
+T+ A Y+ K + K+ +G G+R+ V N G +SY DE D + NG
Sbjct: 3 ITEAAQAYLAKLLAKQNEGTGIRVFVVNPGTPYAECCVSYCPP--DEVEPSDIKLEFNGF 60
Query: 154 QIFINEKDLLYFNGIELDFEFDGLNKGFKFKNPNIK 189
+++ + +DF D + K PN K
Sbjct: 61 SAYVDALSAPFLEDAVIDFVTDRMGGQLTLKAPNAK 96
>gnl|CDD|227178 COG4841, COG4841, Uncharacterized protein conserved in bacteria
[Function unknown].
Length = 95
Score = 31.7 bits (72), Expect = 0.065
Identities = 25/81 (30%), Positives = 38/81 (46%), Gaps = 6/81 (7%)
Query: 98 VTKKAAK-YINKYIQKRGKGIGLRLGVYNRGCSGLS--YKLEYVDEKRKEDQVF-KLNGV 153
VT +A K + + + G + R V GCS L + L E KE + +G+
Sbjct: 5 VTDQALKWFKEELDLEEGNKV--RFFVRYGGCSSLQQGFSLGVAKEVPKEIGYKQEYDGL 62
Query: 154 QIFINEKDLLYFNGIELDFEF 174
FI EKDL YF+ +L ++
Sbjct: 63 TFFIEEKDLWYFDDHDLKVDY 83
>gnl|CDD|237178 PRK12705, PRK12705, hypothetical protein; Provisional.
Length = 508
Score = 32.0 bits (73), Expect = 0.19
Identities = 10/46 (21%), Positives = 23/46 (50%), Gaps = 1/46 (2%)
Query: 81 TLDEAMSIKNTDIAE-ELVTKKAAKYINKYIQKRGKGIGLRLGVYN 125
TL++ ++ A E +KA + + I + G+ + LG+++
Sbjct: 257 TLEKLLADGRIHPARIEEYVQKANEEFKQKIYEIGEEVLEELGIFD 302
>gnl|CDD|240159 cd05120, APH_ChoK_like, Aminoglycoside 3'-phosphotransferase
(APH) and Choline Kinase (ChoK) family. The APH/ChoK
family is part of a larger superfamily that includes
the catalytic domains of other kinases, such as the
typical serine/threonine/tyrosine protein kinases
(PKs), RIO kinases, actin-fragmin kinase (AFK), and
phosphoinositide 3-kinase (PI3K). The family is
composed of APH, ChoK, ethanolamine kinase (ETNK),
macrolide 2'-phosphotransferase (MPH2'), an unusual
homoserine kinase, and uncharacterized proteins with
similarity to the N-terminal domain of acyl-CoA
dehydrogenase 10 (ACAD10). The members of this family
catalyze the transfer of the gamma-phosphoryl group
from ATP (or CTP) to small molecule substrates such as
aminoglycosides, macrolides, choline, ethanolamine, and
homoserine. Phosphorylation of the antibiotics,
aminoglycosides and macrolides, leads to their
inactivation and to bacterial antibiotic resistance.
Phosphorylation of choline, ethanolamine, and
homoserine serves as precursors to the synthesis of
important biological compounds, such as the major
phospholipids, phosphatidylcholine and
phosphatidylethanolamine and the amino acids,
threonine, methionine, and isoleucine.
Length = 155
Score = 30.8 bits (70), Expect = 0.21
Identities = 16/41 (39%), Positives = 23/41 (56%)
Query: 59 KTYGCGSAIASSSLVTEWVKGKTLDEAMSIKNTDIAEELVT 99
K G + S L+ EW++G+TLDE + DIAE+L
Sbjct: 57 KVLASGESDGWSYLLMEWIEGETLDEVSEEEKEDIAEQLAE 97
>gnl|CDD|223169 COG0091, RplV, Ribosomal protein L22 [Translation, ribosomal
structure and biogenesis].
Length = 120
Score = 29.5 bits (67), Expect = 0.55
Identities = 15/43 (34%), Positives = 25/43 (58%), Gaps = 6/43 (13%)
Query: 70 SSLVTEWVKGKTLDEAMSIKNTDIAEELVTKKAAKYINKYIQK 112
+ LV + ++GK + EA++I E V KKAAK + K ++
Sbjct: 25 ARLVADLIRGKKVAEALAI------LEFVPKKAAKLVKKVLES 61
>gnl|CDD|178335 PLN02734, PLN02734, glycyl-tRNA synthetase.
Length = 684
Score = 30.5 bits (69), Expect = 0.69
Identities = 10/18 (55%), Positives = 14/18 (77%)
Query: 155 IFINEKDLLYFNGIELDF 172
IF+N +DL Y+NG +L F
Sbjct: 259 IFVNFRDLYYYNGGKLPF 276
>gnl|CDD|183027 PRK11190, PRK11190, Fe/S biogenesis protein NfuA; Provisional.
Length = 192
Score = 29.6 bits (67), Expect = 0.75
Identities = 24/97 (24%), Positives = 41/97 (42%), Gaps = 8/97 (8%)
Query: 98 VTKKAAKYINKYIQKRGKGIGLRLGVYNRGCS----GLSY-KLEYVDEKRKEDQVFKLNG 152
++ A + K + + +G +R+ V N G G+SY + V+ D K +G
Sbjct: 4 ISDAAQAHFAKLLANQEEGTQIRVFVINPGTPNAECGVSYCPPDAVEA---TDTELKFDG 60
Query: 153 VQIFINEKDLLYFNGIELDFEFDGLNKGFKFKNPNIK 189
+++E + E+DF D L K PN K
Sbjct: 61 FSAYVDELSAPFLEDAEIDFVTDQLGSQLTLKAPNAK 97
>gnl|CDD|238205 cd00336, Ribosomal_L22, Ribosomal protein L22/L17e. L22 (L17 in
eukaryotes) is a core protein of the large ribosomal
subunit. It is the only ribosomal protein that
interacts with all six domains of 23S rRNA, and is one
of the proteins important for directing the proper
folding and stabilizing the conformation of 23S rRNA.
L22 is the largest protein contributor to the surface of
the polypeptide exit channel, the tunnel through which
the polypeptide product passes. L22 is also one of six
proteins located at the putative translocon binding site
on the exterior surface of the ribosome.
Length = 105
Score = 27.5 bits (62), Expect = 2.0
Identities = 13/35 (37%), Positives = 21/35 (60%), Gaps = 6/35 (17%)
Query: 77 VKGKTLDEAMSIKNTDIAEELVTKKAAKYINKYIQ 111
++G ++DEA++ E V KKAAK I K ++
Sbjct: 22 IRGMSVDEALAQL------EFVPKKAAKIILKLLK 50
>gnl|CDD|234631 PRK00098, PRK00098, GTPase RsgA; Reviewed.
Length = 298
Score = 28.2 bits (64), Expect = 2.8
Identities = 13/38 (34%), Positives = 17/38 (44%), Gaps = 8/38 (21%)
Query: 18 GVFEKNDNTVGTGMVGAPACGDVMKLQIKVNKNGVITD 55
G F K NT PA GD ++ + N GVI +
Sbjct: 29 GKFRKKTNT--------PAVGDRVEFSAENNDEGVILE 58
>gnl|CDD|214685 smart00479, EXOIII, exonuclease domain in DNA-polymerase alpha and
epsilon chain, ribonuclease T and other exonucleases.
Length = 169
Score = 27.3 bits (61), Expect = 3.7
Identities = 10/59 (16%), Positives = 19/59 (32%), Gaps = 4/59 (6%)
Query: 136 EYVDEKRKEDQVFKLNGVQIFINEKDLLYFNGIELDFEFDGLNKGFKFKNPNIKNKCGC 194
E +D+ ++V + + F+ + L+ N D F L K
Sbjct: 59 EMLDDAPTFEEVLEE--LLEFLRGRILVAGNSAHFDLRF--LKLEHPRLGIKQPPKLPV 113
>gnl|CDD|219729 pfam08148, DSHCT, DSHCT (NUC185) domain. This C terminal domain is
found in DOB1/SK12/helY-like DEAD box helicases.
Length = 178
Score = 27.2 bits (61), Expect = 4.2
Identities = 8/24 (33%), Positives = 13/24 (54%), Gaps = 2/24 (8%)
Query: 72 LVTEWVKGKTLDEAMSIKNTDIAE 95
+V EW +G + E + TD+ E
Sbjct: 105 VVYEWARGASFSEIC--EETDLFE 126
>gnl|CDD|143988 pfam00237, Ribosomal_L22, Ribosomal protein L22p/L17e. This family
includes L22 from prokaryotes and chloroplasts and L17
from eukaryotes.
Length = 105
Score = 26.3 bits (59), Expect = 5.2
Identities = 14/35 (40%), Positives = 23/35 (65%), Gaps = 6/35 (17%)
Query: 77 VKGKTLDEAMSIKNTDIAEELVTKKAAKYINKYIQ 111
++GK+++EA++I E V KKAAK I K ++
Sbjct: 20 IRGKSVEEALAIL------EFVPKKAAKIILKLLK 48
>gnl|CDD|130988 TIGR01933, hflK, HflK protein. HflK and HflC are paralogs encoded
by tandem genes in Proteobacteria, spirochetes, and some
other bacterial lineages. The HflKC complex is anchored
in the membrane and exposed to the periplasm. The
complex is not active as a protease, but rather binds to
and appears to modulate the ATP-dependent protease FtsH.
The overall function of HflKC is not fully
described.//Regulation of FtsH by HflKC appears to be
negative (PMID:8947034,PMID:96367) [SS 8/27/03].
Length = 261
Score = 27.4 bits (61), Expect = 5.6
Identities = 10/31 (32%), Positives = 18/31 (58%), Gaps = 1/31 (3%)
Query: 115 KGIGLRLGVYNRGC-SGLSYKLEYVDEKRKE 144
+G+ LR G Y+R GL++K +++E
Sbjct: 9 RGVVLRFGKYHRTVDPGLNWKPPFIEEVYPV 39
>gnl|CDD|211382 cd11010, S1-P1_nuclease, S1/P1 nucleases and related enzymes. This
family summarizes both S1 and P1 nucleases (EC:3.1.30.1)
which cleave RNA and single stranded DNA with no base
specificity. S1 nuclease is more active on DNA than RNA.
Its reaction products are oligonucleotides or single
nucleotides with 5' phosphoryl groups. Although its
primary substrate is single-stranded, it may also
introduce single-stranded breaks in double-stranded DNA
or RNA, or DNA-RNA hybrids. It is used as a reagent in
nuclease protection assays and in removing single
stranded tails from DNA molecules to create blunt ended
molecules and opening hairpin loops generated during
synthesis of double stranded cDNA. P1 nuclease cleaves
its substrate at every position yielding nucleoside 5'
monophosphates, and it does not recognize or act on
double-stranded DNA. It is useful at removing single
stranded strands hanging off the end of double stranded
DNA and at completely cleaving melted DNA for simple DNA
composition analysis.
Length = 249
Score = 27.0 bits (60), Expect = 6.2
Identities = 7/21 (33%), Positives = 14/21 (66%)
Query: 92 DIAEELVTKKAAKYINKYIQK 112
+IAE+ +T KA K +++ +
Sbjct: 11 EIAEQYLTPKARKAVDRLLGG 31
>gnl|CDD|240903 cd12457, RRM_XMAS2, RNA recognition motif in X-linked male sterile
2 (Xmas-2) and similar proteins. This subfamily
corresponds to the RRM in Xmas-2, the Drosophila homolog
of yeast Sac3p protein, together with E(y)2, the
Drosophila homologue of yeast Sus1p protein, forming an
endogenous complex that is required in the regulation of
mRNA transport and also involved in the efficient
transcription regulation of the heat-shock protein 70
(hsp70) loci. All family members are found in insects
and contain an N-terminal RNA recognition motif (RRM),
also termed RBD (RNA binding domain) or RNP
(ribonucleoprotein domain), followed by a PCI domain.
Length = 71
Score = 25.0 bits (55), Expect = 8.1
Identities = 13/29 (44%), Positives = 19/29 (65%), Gaps = 3/29 (10%)
Query: 87 SIKNTDIAEELVTKKAAKYINKYIQKRGK 115
SIK T++ E L+TK AK KY ++ G+
Sbjct: 2 SIKCTNVPELLLTKDIAK---KYFRRFGR 27
>gnl|CDD|212982 cd12049, SH3_DOCK4_B, Src Homology 3 domain of Class B Dedicator of
Cytokinesis 4. Dock4 is a class B DOCK and is an
atypical guanine nucleotide exchange factor (GEF) that
lacks the conventional Dbl homology (DH) domain. It
plays a role in regulating dendritic growth and
branching in hippocampal neurons, where it is highly
expressed. It may also regulate spine morphology and
synapse formation. Dock4 activates the Ras family GTPase
Rap1, probably indirectly through interaction with Rap
regulatory proteins. All DOCKs contain two homology
domains: the DHR-1 (Dock homology region-1), also called
CZH1 (CED-5, Dock180, and MBC-zizimin homology 1), and
DHR-2 (also called CZH2 or Docker). The DHR-1 domain
binds phosphatidylinositol-3,4,5-triphosphate while
DHR-2 contains the catalytic activity for Rac and/or
Cdc42. Class B DOCKs also contain an SH3 domain at the
N-terminal region and a PxxP motif at the C-terminus.
The SH3 domain of Dock4 binds to DHR-2 in an
autoinhibitory manner; binding of the scaffold protein
Elmo to the SH3 domain of Dock4 exposes the DHR-2 domain
and promotes GEF activity. SH3 domains are protein
interaction domains that bind to proline-rich ligands
with moderate affinity and selectivity, preferentially
to PxxP motifs. They play versatile and diverse roles in
the cell including the regulation of enzymes, changing
the subcellular localization of signaling pathway
components, and mediating the formation of multiprotein
complex assemblies.
Length = 56
Score = 24.8 bits (54), Expect = 8.5
Identities = 8/15 (53%), Positives = 11/15 (73%)
Query: 175 DGLNKGFKFKNPNIK 189
+G +GF KNPN+K
Sbjct: 31 EGWYRGFALKNPNVK 45
>gnl|CDD|217964 pfam04205, FMN_bind, FMN-binding domain. This conserved region
includes the FMN-binding site of the NqrC protein as
well as the NosR and NirI regulatory proteins.
Length = 84
Score = 25.3 bits (56), Expect = 9.2
Identities = 14/60 (23%), Positives = 25/60 (41%), Gaps = 6/60 (10%)
Query: 38 GDVMKLQIKVNKNGVITDAKFK----TYGCGSAIASSSLVTEWVKGKTLDEAMSIKNTDI 93
G + + + V+K+G IT + T G G + ++V GK L + D+
Sbjct: 3 GGPITVTVTVDKDGKITGVEVLEHKETPGLGDKAEDEEFIKQFV-GKQLTAV-KKDSADV 60
>gnl|CDD|239722 cd03753, proteasome_alpha_type_5, proteasome_alpha_type_5. The 20S
proteasome, multisubunit proteolytic complex, is the
central enzyme of nonlysosomal protein degradation in
both the cytosol and nucleus. It is composed of 28
subunits arranged as four homoheptameric rings that
stack on top of one another forming an elongated
alpha-beta-beta-alpha cylinder with a central cavity.
The proteasome alpha and beta subunits are members of
the N-terminal nucleophile (Ntn)-hydrolase superfamily.
Their N-terminal threonine residues are exposed as a
nucleophile in peptide bond hydrolysis. Mammals have 7
alpha and 7 beta proteasome subunits while archaea have
one of each.
Length = 213
Score = 26.5 bits (59), Expect = 9.3
Identities = 15/35 (42%), Positives = 18/35 (51%)
Query: 51 GVITDAKFKTYGCGSAIASSSLVTEWVKGKTLDEA 85
G T K G GS A SSL ++ K TL+EA
Sbjct: 153 GTFTRCDAKAIGSGSEGAQSSLQEKYHKDMTLEEA 187
>gnl|CDD|227355 COG5022, COG5022, Myosin heavy chain [Cytoskeleton].
Length = 1463
Score = 27.0 bits (60), Expect = 9.7
Identities = 8/19 (42%), Positives = 14/19 (73%)
Query: 43 LQIKVNKNGVITDAKFKTY 61
++I+ ++NG I AK +TY
Sbjct: 222 IKIEFDENGEICGAKIETY 240
Database: CDD.v3.10
Posted date: Mar 20, 2013 7:55 AM
Number of letters in database: 10,937,602
Number of sequences in database: 44,354
Lambda K H
0.316 0.137 0.398
Gapped
Lambda K H
0.267 0.0734 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 44354
Number of Hits to DB: 9,948,398
Number of extensions: 917139
Number of successful extensions: 1011
Number of sequences better than 10.0: 1
Number of HSP's gapped: 996
Number of HSP's successfully gapped: 53
Length of query: 200
Length of database: 10,937,602
Length adjustment: 92
Effective length of query: 108
Effective length of database: 6,857,034
Effective search space: 740559672
Effective search space used: 740559672
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.3 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.6 bits)
S2: 56 (25.3 bits)